Research articles

CellRank enables cell fate mapping from single-cell RNA sequencing data in a consistent and scalable manner, relying on different views of the data such as pseudotime or stemness potential, RNA velocity and experimental time points.

The authors provide a suite of in vitro protocols through which mouse and human pluripotent stem cells, mouse blastocysts and human blastoids can be reversibly induced to enter a diapause-like dormant state via pharmacological inhibition of mTOR

Investigating mechanical forces during angiogenic sprouting by three-dimensional traction force microscopy (TFM) in hydrogel matrices, including steps to analyze and interpret cell–extracellular matrix forces using open-source TFMLAB software.

This protocol isolates lignin from various types of biomass, screens for high-quality lignins, and uses them to directly prepare lignin adhesives without chemical modification, the performance of which is then assessed. It produces lignin adhesives with light colors and superior properties.

This protocol details transsynaptic tracing approaches using retrograde and anterograde viral tracers to map and manipulate neuron–tumor circuits in xenografts, brain organoid models and co-cultures.

Urea, formamide, cyclohexanone oxime and amino acids are vital raw materials. Their synthesis often requires high temperatures and dangerous reagents. This protocol describes an aqueous electrocatalytic approach using inorganic nitrogen sources.

This protocol covers a package for running statistical testing on the temporal dynamics of neural activity data obtained from various functional neural recording modalities.

GPSeq is a genome-wide method for probing the radial organization of the genome in cells or nuclei by progressive in situ digestion of chromatin with a restriction enzyme diffusing inward from the periphery followed by high-throughput sequencing.

Here Plikus and colleagues provide a step-by-step protocol for the isolation and characterization of lipocartilage from mouse ear and the purification of its lipochondrocytes.

We present a protocol for high-resolution genome-wide mapping of nascent RNA polymerase II transcription initiation of both stable RNAs and transiently expressed RNAs using total RNA from diverse sample types.

This protocol describes inverse toeprinting coupled to next-generation sequencing, an in vitro approach to characterize bacterial translation at codon resolution that can accommodate custom synthetic libraries and various translation perturbations.

Upconversion particle-based holographic fluorescence optical tweezers enable super-resolved photonic force microscopy and applications on long-range subfemtonewton force sensing, intracellular viscosity measurements and temperature sensing.

This protocol describes a flexible workflow for joint profiling of chromatin accessibility and transcriptomes in single nuclei, compatible with either plate or droplet single-cell isolation platforms.

A strategy for isolating Escherichia coli ribosome–nascent chain complexes and analyzing their conformational dynamics and interactors at peptide level using hydrogen–deuterium exchange mass spectrometry is presented.

In this protocol, the authors explain how to set up and use the cloud-based Precision Health Integrated Diagnostic (PHIND) system, a smart-toilet-based platform for passive and automated defecation monitoring to provide continuous gut health information.

This protocol covers the acoustics-based separation of biological particles such as viruses and single extracellular vesicles from biofluids, including plasma and saliva, with high purity.

We present a protocol for the acquisition and analysis of in vivo Raman spectra to extract biochemical information from tissues for biomedical applications.